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LIMS2 LIM zinc finger domain containing 2 [ Homo sapiens (human) ]

Gene ID: 55679, updated on 1-Jun-2020

Summary

Official Symbol
LIMS2provided by HGNC
Official Full Name
LIM zinc finger domain containing 2provided by HGNC
Primary source
HGNC:HGNC:16084
See related
Ensembl:ENSG00000072163 MIM:607908
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LGMD2W; PINCH2; MDRCMTT; PINCH-2
Summary
This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Broad expression in endometrium (RPKM 24.9), fat (RPKM 20.9) and 23 other tissues See more
Orthologs

Genomic context

See LIMS2 in Genome Data Viewer
Location:
2q14.3
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (127638381..127681786, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (128395996..128439360, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373609 Neighboring gene myosin VIIB Neighboring gene uncharacterized LOC101927834 Neighboring gene G protein-coupled receptor 17 Neighboring gene SFT2 domain containing 3 Neighboring gene WD repeat domain 33 Neighboring gene RNY4 pseudogene 7

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Muscular dystrophy, limb-girdle, type 2W
MedGen: C4225192 OMIM: 616827 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10044

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell junction assembly TAS
Traceable Author Statement
more info
 
cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of hepatocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of integrin-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of substrate adhesion-dependent cell spreading IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
focal adhesion HDA PubMed 
focal adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
focal adhesion IDA
Inferred from Direct Assay
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
LIM and senescent cell antigen-like-containing domain protein 2
Names
ILK-binding protein
LIM and senescent cell antigen-like domains 2
LIM-type zinc finger domains 2
particularly interesting new Cys-His protein 2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042235.1 RefSeqGene

    Range
    5001..48366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001136037.3NP_001129509.2  LIM and senescent cell antigen-like-containing domain protein 2 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This transcript represents variant 1 and encodes isoform 1.
    Source sequence(s)
    AC010976, AC074114, AK022470, AK055363, BC065816, CA439343, DC356496, DR006887
    Consensus CDS
    CCDS54396.1
    UniProtKB/Swiss-Prot
    Q7Z4I7
    UniProtKB/TrEMBL
    B3KNZ3
    Related
    ENSP00000443794.2, ENST00000545738.6
    Conserved Domains (5) summary
    cd09331
    Location:3795
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:98149
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:162212
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:218271
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:279332
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  2. NM_001161403.3NP_001154875.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001154875.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC010976, AC074114, BC065816, DR006887
    Consensus CDS
    CCDS54395.1
    UniProtKB/Swiss-Prot
    Q7Z4I7
    Related
    ENSP00000347240.4, ENST00000355119.8
    Conserved Domains (5) summary
    cd09331
    Location:1573
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:76127
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:140190
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:196249
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:257310
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  3. NM_001161404.1NP_001154876.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 5

    See identical proteins and their annotated locations for NP_001154876.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AC010976, AF527766, CA439343, DA890151
    Consensus CDS
    CCDS54394.1
    UniProtKB/Swiss-Prot
    Q7Z4I7
    UniProtKB/TrEMBL
    A0A024RAH1
    Related
    ENSP00000387002.1, ENST00000410011.5
    Conserved Domains (5) summary
    cd09331
    Location:1068
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:71122
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:135185
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:191244
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:252305
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  4. NM_001256542.1NP_001243471.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001243471.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AF527770, BX458594, CA439343, DA848179
    Consensus CDS
    CCDS58725.1
    UniProtKB/Swiss-Prot
    Q7Z4I7
    Related
    ENSP00000386570.1, ENST00000410038.5
    Conserved Domains (3) summary
    cd09334
    Location:4497
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:105158
    LIM5_PINCH; The fifth LIM domain of protein PINCH
    cl02475
    Location:238
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  5. NM_017980.4NP_060450.2  LIM and senescent cell antigen-like-containing domain protein 2 isoform 2

    See identical proteins and their annotated locations for NP_060450.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AC074114, AF527764, AF527765, BP221000, CA439343
    Consensus CDS
    CCDS2147.1
    UniProtKB/Swiss-Prot
    Q7Z4I7
    Related
    ENSP00000326888.5, ENST00000324938.9
    Conserved Domains (5) summary
    cd09331
    Location:3997
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:100151
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:164214
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:220273
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:281334
    LIM5_PINCH; The fifth LIM domain of protein PINCH

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    127638381..127681786 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005263710.2XP_005263767.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X3

    Conserved Domains (4) summary
    cd09332
    Location:758
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:71121
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:127180
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:188241
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  2. XM_006712627.4XP_006712690.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X5

    Conserved Domains (3) summary
    cd09333
    Location:2474
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:80133
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:141194
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  3. XM_024452983.1XP_024308751.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X1

    Related
    ENSP00000386637.2, ENST00000409808.6
    Conserved Domains (5) summary
    cd09331
    Location:1068
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:71122
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:135185
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:191244
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:252305
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  4. XM_011511453.1XP_011509755.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X2

    Conserved Domains (4) summary
    cd09331
    Location:3997
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:100151
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09335
    Location:240293
    LIM5_PINCH; The fifth LIM domain of protein PINCH
    cl02475
    Location:164205
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  5. XM_024452984.1XP_024308752.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X1

    Conserved Domains (5) summary
    cd09331
    Location:1068
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:71122
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:135185
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:191244
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:252305
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  6. XM_024452986.1XP_024308754.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X7

    Related
    ENSP00000386252.1, ENST00000409286.5
    Conserved Domains (3) summary
    cd09334
    Location:4497
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:105158
    LIM5_PINCH; The fifth LIM domain of protein PINCH
    cl02475
    Location:238
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  7. XM_024452985.1XP_024308753.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X7

    Conserved Domains (3) summary
    cd09334
    Location:4497
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:105158
    LIM5_PINCH; The fifth LIM domain of protein PINCH
    cl02475
    Location:238
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  8. XM_017004469.1XP_016859958.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X4

  9. XM_006712628.3XP_006712691.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X6

    Conserved Domains (2) summary
    cd09331
    Location:3997
    LIM1_PINCH; The first LIM domain of protein PINCH
    cd09332
    Location:100143
    LIM2_PINCH; The second LIM domain of protein PINCH

RNA

  1. XR_922961.2 RNA Sequence

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